This should be governed by a simple formula. Basically, the decision to turn on Fortress Shield is made when the following condition is met:
Expected hard flux increase from effective (shield-mitigated) damage during time window (x) > fixed Fortress Shield hard flux increase during same time window (x)
This is probably what Alex is using in terms of Fortress Shield AI, but the calculation of the first term is quite complex, as it has to factor in - damage type, shield efficiency, crew levels, skill perks, missile trajectory and expected effectiveness of point defense systems.
An error or oversight in any of these terms could be what's causing what we observe. Or maybe Alex did something else entirely different that us mortals cannot comprehend.